Redox hot spots occurring as metal-rich anoxic groundwater discharges through oxic wetland and river sediments commonly result in the formation of iron (Fe) oxide precipitates. These redox-sensitive precipitates influence the release of nutrients and metals to surface water and can act as ‘contaminant sponges’ by absorbing toxic compounds. We explore the feasibility of a non-invasive, high-resolution magnetic susceptibility (MS) technique to efficiently map the spatial variations of magnetic Fe oxide precipitates in the shallow bed of three rivers impacted by anoxic groundwater discharge. Laboratory analyses on Mashpee River (MA, USA) sediments demonstrate the sensitivity of MS to sediment Fe concentrations. Field surveys in the Mashpee and Quashnet rivers (MA, USA) reveal several discrete high MS zones, which are associated with likely anoxic groundwater discharge as evaluated by riverbed temperature, vertical head gradient, and groundwater chemistry measurements. In the East River (CO, USA), widespread cobbles/rocks exhibit high background MS from geological ferrimagnetic minerals, thereby obscuring the relatively small enhancement of MS from groundwater induced Fe oxide precipitates. Our study suggests that, in settings with low geological sources of magnetic minerals such as lowland rivers and wetlands, MS may serve as a complementary tool to temperature methods for efficiently mapping Fe oxide accumulation zones due to anoxic groundwater discharges that may function as biogeochemical hot spots and water quality control points in gaining systems.